Wednesday, August 05, 2015

An Introduction to Molecular Dynamics

Saturday, April 25, 2015

QCWO


HEADER    UNCLASSIFIED                            25-Apr-15
TITLE     ALL ATOM STRUCTURE FOR MOLECULE UNK                                   
AUTHOR    GROMOS AUTOMATIC TOPOLOGY BUILDER REVISION 2015-03-06
AUTHOR   2  http://compbio.biosci.uq.edu.au/atb
HETATM    1   O3 QCWO    0      -6.629  -1.565  -1.580  1.00  0.00           O
HETATM    2   S1 QCWO    0      -7.182  -0.859  -0.079  1.00  0.00           S
HETATM    3   O1 QCWO    0      -8.883   0.153  -0.543  1.00  0.00           O
HETATM    4   O2 QCWO    0      -6.708  -2.285   1.295  1.00  0.00           O
HETATM    5   C6 QCWO    0      -5.956   0.482   0.170  1.00  0.00           C
HETATM    6   C7 QCWO    0      -6.394   1.672   0.564  1.00  0.00           C
HETATM    7   H4 QCWO    0      -7.451   1.875   0.681  1.00  0.00           H
HETATM    8   C2 QCWO    0      -5.417   2.747   0.827  1.00  0.00           C
HETATM    9   N1 QCWO    0      -5.805   3.958   1.180  1.00  0.00           N
HETATM   10   H1 QCWO    0      -5.068   4.663   1.323  1.00  0.00           H
HETATM   11   C1 QCWO    0      -7.207   4.413   1.382  1.00  0.00           C
HETATM   12   H1 QCWO    0      -7.681   3.816   2.163  1.00  0.00           H
HETATM   13   H2 QCWO    0      -7.763   4.321   0.448  1.00  0.00           H
HETATM   14   H3 QCWO    0      -7.169   5.456   1.688  1.00  0.00           H
HETATM   15   C3 QCWO    0      -3.980   2.469   0.657  1.00  0.00           C
HETATM   16   H2 QCWO    0      -3.294   3.289   0.829  1.00  0.00           H
HETATM   17   C4 QCWO    0      -3.560   1.260   0.300  1.00  0.00           C
HETATM   18   H3 QCWO    0      -2.500   1.072   0.153  1.00  0.00           H
HETATM   19   C5 QCWO    0      -4.504   0.141   0.021  1.00  0.00           C
HETATM   20   N2 QCWO    0      -4.214  -1.062  -0.354  1.00  0.00           N
HETATM   21   H5 QCWO    0      -5.735  -1.915  -1.296  1.00  0.00           H
HETATM   22   C8 QCWO    0      -2.829  -1.523  -0.371  1.00  0.00           C
HETATM   23   C9 QCWO    0      -2.342  -2.148  -1.517  1.00  0.00           C
HETATM   24   H6 QCWO    0      -2.962  -2.209  -2.403  1.00  0.00           H
HETATM   25  C13 QCWO    0      -2.048  -1.462   0.784  1.00  0.00           C
HETATM   26   H9 QCWO    0      -2.446  -1.011   1.684  1.00  0.00           H
HETATM   27  C12 QCWO    0      -0.781  -2.014   0.781  1.00  0.00           C
HETATM   28   H8 QCWO    0      -0.180  -1.980   1.681  1.00  0.00           H
HETATM   29  C11 QCWO    0      -0.272  -2.618  -0.369  1.00  0.00           C
HETATM   30  C10 QCWO    0      -1.061  -2.673  -1.518  1.00  0.00           C
HETATM   31   H7 QCWO    0      -0.671  -3.149  -2.408  1.00  0.00           H
HETATM   32   N3 QCWO    0       1.059  -3.237  -0.379  1.00  0.00           N
HETATM   33  H10 QCWO    0       1.164  -3.778   0.492  1.00  0.00           H
HETATM   34  C14 QCWO    0       2.173  -2.293  -0.450  1.00  0.00           C
HETATM   35  C15 QCWO    0       2.197  -1.269  -1.397  1.00  0.00           C
HETATM   36  H11 QCWO    0       1.357  -1.136  -2.064  1.00  0.00           H
HETATM   37  C19 QCWO    0       3.269  -2.457   0.387  1.00  0.00           C
HETATM   38  H13 QCWO    0       3.276  -3.253   1.121  1.00  0.00           H
HETATM   39  C18 QCWO    0       4.358  -1.604   0.295  1.00  0.00           C
HETATM   40   S2 QCWO    0       5.747  -1.837   1.468  1.00  0.00           S
HETATM   41   O4 QCWO    0       5.269  -0.820   3.056  1.00  0.00           O
HETATM   42   O5 QCWO    0       5.969  -3.755   1.674  1.00  0.00           O
HETATM   43   O6 QCWO    0       7.182  -1.038   0.639  1.00  0.00           O
HETATM   44  C17 QCWO    0       4.397  -0.565  -0.646  1.00  0.00           C
HETATM   45  C16 QCWO    0       3.290  -0.432  -1.495  1.00  0.00           C
HETATM   46  H12 QCWO    0       3.300   0.342  -2.250  1.00  0.00           H
HETATM   47   N4 QCWO    0       5.592   0.211  -0.790  1.00  0.00           N
HETATM   48  H14 QCWO    0       6.389  -0.255  -0.196  1.00  0.00           H
HETATM   49  C20 QCWO    0       5.544   1.637  -0.714  1.00  0.00           C
HETATM   50  C25 QCWO    0       4.392   2.403  -0.536  1.00  0.00           C
HETATM   51  H18 QCWO    0       3.434   1.920  -0.421  1.00  0.00           H
HETATM   52  C21 QCWO    0       6.767   2.323  -0.824  1.00  0.00           C
HETATM   53  H15 QCWO    0       7.675   1.749  -0.951  1.00  0.00           H
HETATM   54  C22 QCWO    0       6.822   3.697  -0.763  1.00  0.00           C
HETATM   55  H16 QCWO    0       7.782   4.194  -0.845  1.00  0.00           H
HETATM   56  C23 QCWO    0       5.667   4.462  -0.594  1.00  0.00           C
HETATM   57  C24 QCWO    0       4.461   3.787  -0.482  1.00  0.00           C
HETATM   58  H17 QCWO    0       3.548   4.351  -0.339  1.00  0.00           H
HETATM   59  C26 QCWO    0       5.738   5.985  -0.542  1.00  0.00           C
HETATM   60  H11 QCWO    0       4.825   6.400  -0.125  1.00  0.00           H
HETATM   61  H21 QCWO    0       5.873   6.405  -1.537  1.00  0.00           H
HETATM   62  H31 QCWO    0       6.574   6.315   0.070  1.00  0.00           H
CONECT    1    2
CONECT    2    1    3    4    5
CONECT    3    2
CONECT    4    2
CONECT    5    2    6   19
CONECT    6    5    7    8
CONECT    7    6
CONECT    8    6    9   15
CONECT    9    8   10   11
CONECT   10    9
CONECT   11    9   12   13   14
CONECT   12   11
CONECT   13   11
CONECT   14   11
CONECT   15    8   16   17
CONECT   16   15
CONECT   17   15   18   19
CONECT   18   17
CONECT   19    5   17   20
CONECT   20   19   21   22
CONECT   21   20
CONECT   22   20   23   25
CONECT   23   22   24   30
CONECT   24   23
CONECT   25   22   26   27
CONECT   26   25
CONECT   27   25   28   29
CONECT   28   27
CONECT   29   27   30   32
CONECT   30   23   29   31
CONECT   31   30
CONECT   32   29   33   34
CONECT   33   32
CONECT   34   32   35   37
CONECT   35   34   36   45
CONECT   36   35
CONECT   37   34   38   39
CONECT   38   37
CONECT   39   37   40   44
CONECT   40   39   41   42   43
CONECT   41   40
CONECT   42   40
CONECT   43   40
CONECT   44   39   45   47
CONECT   45   35   44   46
CONECT   46   45
CONECT   47   44   48   49
CONECT   48   47
CONECT   49   47   50   52
CONECT   50   49   51   57
CONECT   51   50
CONECT   52   49   53   54
CONECT   53   52
CONECT   54   52   55   56
CONECT   55   54
CONECT   56   54   57   59
CONECT   57   50   56   58
CONECT   58   57
CONECT   59   56   60   61   62
CONECT   60   59
CONECT   61   59
CONECT   62   59
END
;----------------------------TITLE -------------------------------------------
;   None
;
; This file was generated at 15:10 on 2015-04-25 by
;
;                  Automatic Topology Builder  
;
;                   REVISION 2015-03-06
;-----------------------------------------------------------------------------
; Authors     : Alpeshkumar K. Malde, Le Zuo, Matthew Breeze, Martin Stroet, Alan E. Mark
;
; Institute   : Molecular Dynamics group, 
;               School of Chemistry and Molecular Biosciences (SCMB),
;               The University of Queensland, QLD 4072, Australia
; URL         : http://compbio.biosci.uq.edu.au/atb
; Citation    : Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.
;               An Automated force field Topology Builder (ATB) and repository: version 1.0.
;               Journal of Chemical Theory and Computation, 2011, 7(12), 4026-4037.
;               http://pubs.acs.org/doi/abs/10.1021/ct200196m
;
; Disclaimer  : 
;      While every effort has been made to ensure the accuracy and validity of parameters provided below
;      the assignment of parameters is being based on an automated procedure combining data provided by a
;      given user as well as calculations performed using third party software. They are provided as a guide.
;      The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided
;      are appropriate for use in any specific application. Users are advised to treat these parameters with discretion
;      and to perform additional validation tests for their specific application if required. Neither the authors
;      of the ATB or The University of Queensland except any responsibly for how the parameters may be used.
;
; Release notes and warnings: 
;  (1) The topology is based on a set of atomic coordinates and other data provided by the user after
;      after quantum mechanical optimization of the structure using different levels of theory depending on
;      the nature of the molecule.
;  (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.
;      In these cases alternative type codes are provided at the end of the line.
;  (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral
;      type code may be incorporated in cases where an exact match could not be found. These are marked as "non-standard"
;      or "uncertain" in comments.
;  (4) In some cases it is not possible to assign an appropriate parameter automatically. "%" is used as a place holder
;      for those fields that could not be determined automatically. The parameters in these fields must be assigned manually
;      before the file can be used.
;-----------------------------------------------------------------------------
; Input Structure : QCWO
; Output          : ALL ATOM topology
; Use in conjunction with the corresponding all atom PDB file.
;----------------------------------------------------------------------------
; Initial Guess Topology Generation: 
; The topology was guessed from HF/STO-3G level in implicit water optimized geometry
; and MULLIKEN charges.
; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.
;
; Topology file generated at 15:04 on 25 Apr 2015 for molecule
; None (IUPAC: [5-(methylamino)-2-{[4-({4-[(4-methylphenyl)amino]-3-(trihydroxy-$l^{4}-sulfanyl)phenyl}amino)phenyl]amino}phenyl]-$l^{4}-sulfanetriol, database identifier: QCWO)
; by Automatic Topology Builder(revision 2015-03-06).
;
[ moleculetype ]
; Name   nrexcl
QCWO     3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
    1    OM    1    QCWO     O3    1   -0.249  15.9994 
    2 SDmso    1    QCWO     S1    1    0.248  32.0600 
    3    OM    1    QCWO     O1    1   -0.249  15.9994 
    4    OM    1    QCWO     O2    1   -0.249  15.9994 
    5     C    1    QCWO     C6    1    0.040  12.0110      ; -0.459
    6     C    1    QCWO     C7    2   -0.094  12.0110 
    7    HC    1    QCWO     H4    2    0.094   1.0080      ;  0.000
    8     C    1    QCWO     C2    3    0.289  12.0110 
    9    NT    1    QCWO     N1    3   -0.230  14.0067 
   10     H    1    QCWO     H1    3    0.315   1.0080 
   11     C    1    QCWO     C1    3   -0.053  12.0110 
   12    HC    1    QCWO     H1    3    0.120   1.0080 
   13    HC    1    QCWO     H2    3    0.120   1.0080 
   14    HC    1    QCWO     H3    3    0.120   1.0080      ;  0.681
   15     C    1    QCWO     C3    4   -0.059  12.0110 
   16    HC    1    QCWO     H2    4    0.122   1.0080 
   17     C    1    QCWO     C4    4    0.003  12.0110 
   18    HC    1    QCWO     H3    4    0.131   1.0080 
   19     C    1    QCWO     C5    4    0.126  12.0110      ;  0.323
   20    NT    1    QCWO     N2    5   -0.195  14.0067 
   21     H    1    QCWO     H5    5    0.269   1.0080 
   22     C    1    QCWO     C8    5    0.073  12.0110 
   23     C    1    QCWO     C9    5   -0.057  12.0110 
   24    HC    1    QCWO     H6    5    0.089   1.0080      ;  0.179
   25     C    1    QCWO    C13    6   -0.057  12.0110 
   26    HC    1    QCWO     H9    6    0.089   1.0080 
   27     C    1    QCWO    C12    6   -0.061  12.0110 
   28    HC    1    QCWO     H8    6    0.086   1.0080      ;  0.057
   29     C    1    QCWO    C11    7    0.104  12.0110 
   30     C    1    QCWO    C10    7   -0.061  12.0110 
   31    HC    1    QCWO     H7    7    0.086   1.0080 
   32    NT    1    QCWO     N3    7   -0.336  14.0067 
   33     H    1    QCWO    H10    7    0.179   1.0080 
   34     C    1    QCWO    C14    7    0.081  12.0110 
   35     C    1    QCWO    C15    7   -0.078  12.0110 
   36    HC    1    QCWO    H11    7    0.069   1.0080      ;  0.044
   37     C    1    QCWO    C19    8   -0.076  12.0110 
   38    HC    1    QCWO    H13    8    0.076   1.0080      ;  0.000
   39     C    1    QCWO    C18    9   -0.045  12.0110 
   40 SDmso    1    QCWO     S2    9    0.057  32.0600 
   41    OM    1    QCWO     O4    9   -0.249  15.9994 
   42    OM    1    QCWO     O5    9   -0.249  15.9994 
   43    OM    1    QCWO     O6    9   -0.249  15.9994      ; -0.735
   44     C    1    QCWO    C17   10    0.094  12.0110 
   45     C    1    QCWO    C16   10   -0.078  12.0110 
   46    HC    1    QCWO    H12   10    0.069   1.0080 
   47    NT    1    QCWO     N4   10   -0.409  14.0067 
   48     H    1    QCWO    H14   10    0.253   1.0080 
   49     C    1    QCWO    C20   10    0.100  12.0110 
   50     C    1    QCWO    C25   10   -0.099  12.0110 
   51    HC    1    QCWO    H18   10    0.057   1.0080      ; -0.013
   52     C    1    QCWO    C21   11   -0.099  12.0110 
   53    HC    1    QCWO    H15   11    0.057   1.0080 
   54     C    1    QCWO    C22   11   -0.070  12.0110 
   55    HC    1    QCWO    H16   11    0.058   1.0080      ; -0.054
   56     C    1    QCWO    C23   12   -0.013  12.0110 
   57     C    1    QCWO    C24   12   -0.070  12.0110 
   58    HC    1    QCWO    H17   12    0.058   1.0080 
   59     C    1    QCWO    C26   12   -0.187  12.0110 
   60    HC    1    QCWO    H11   12    0.063   1.0080 
   61    HC    1    QCWO    H21   12    0.063   1.0080 
   62    HC    1    QCWO    H31   12    0.063   1.0080      ; -0.023
; total charge of the molecule:   0.000
[ bonds ]
;  ai   aj  funct   c0         c1
    1    2    2   0.1740   2.6700e+06
    2    3    2   0.2040   5.0300e+06
    2    4    2   0.2040   5.0300e+06
    2    5    2   0.1830   5.6200e+06
    5    6    2   0.1330   1.1800e+07
    5   19    2   0.1520   5.4300e+06
    6    7    2   0.1090   1.2300e+07
    6    8    2   0.1480   5.7300e+06
    8    9    2   0.1320   1.2000e+07
    8   15    2   0.1470   8.7100e+06
    9   10    2   0.1000   1.8700e+07
    9   11    2   0.1480   5.7300e+06
   11   12    2   0.1090   1.2300e+07
   11   13    2   0.1090   1.2300e+07
   11   14    2   0.1090   1.2300e+07
   15   16    2   0.1090   1.2300e+07
   15   17    2   0.1330   1.1800e+07
   17   18    2   0.1090   1.2300e+07
   17   19    2   0.1520   5.4300e+06
   19   20    2   0.1320   1.2000e+07
   20   21    2   0.1980   6.4000e+05
   20   22    2   0.1470   8.7100e+06
   22   23    2   0.1390   8.6600e+06
   22   25    2   0.1390   8.6600e+06
   23   24    2   0.1090   1.2300e+07
   23   30    2   0.1390   8.6600e+06
   25   26    2   0.1090   1.2300e+07
   25   27    2   0.1390   8.6600e+06
   27   28    2   0.1090   1.2300e+07
   27   29    2   0.1390   8.6600e+06
   29   30    2   0.1390   8.6600e+06
   29   32    2   0.1470   8.7100e+06
   30   31    2   0.1090   1.2300e+07
   32   33    2   0.1000   1.8700e+07
   32   34    2   0.1470   8.7100e+06
   34   35    2   0.1390   8.6600e+06
   34   37    2   0.1390   8.6600e+06
   35   36    2   0.1090   1.2300e+07
   35   45    2   0.1390   8.6600e+06
   37   38    2   0.1090   1.2300e+07
   37   39    2   0.1390   8.6600e+06
   39   40    2   0.1830   5.6200e+06
   39   44    2   0.1390   8.6600e+06
   40   41    2   0.1940   1.3300e+06
   40   42    2   0.1940   1.3300e+06
   40   43    2   0.1840   1.0600e+06
   44   45    2   0.1390   8.6600e+06
   44   47    2   0.1400   8.5400e+06
   45   46    2   0.1090   1.2300e+07
   47   48    2   0.1100   1.2100e+07
   47   49    2   0.1400   8.5400e+06
   49   50    2   0.1390   8.6600e+06
   49   52    2   0.1390   8.6600e+06
   50   51    2   0.1090   1.2300e+07
   50   57    2   0.1390   8.6600e+06
   52   53    2   0.1090   1.2300e+07
   52   54    2   0.1390   8.6600e+06
   54   55    2   0.1090   1.2300e+07
   54   56    2   0.1390   8.6600e+06
   56   57    2   0.1390   8.6600e+06
   56   59    2   0.1530   7.1500e+06
   57   58    2   0.1090   1.2300e+07
   59   60    2   0.1090   1.2300e+07
   59   61    2   0.1090   1.2300e+07
   59   62    2   0.1090   1.2300e+07
[ pairs ]
;  ai   aj  funct  ;  all 1-4 pairs but the ones excluded in GROMOS itp
    1    6    1
    1   19    1
    3    6    1
    3   19    1
    4    6    1
    4   19    1
    5   21    1
    5   22    1
    6   10    1
    6   11    1
    8   12    1
    8   13    1
    8   14    1
   10   12    1
   10   13    1
   10   14    1
   10   15    1
   11   15    1
   17   21    1
   17   22    1
   19   23    1
   19   25    1
   21   23    1
   21   25    1
   27   33    1
   27   34    1
   29   35    1
   29   37    1
   30   33    1
   30   34    1
   33   35    1
   33   37    1
   37   41    1
   37   42    1
   37   43    1
   39   48    1
   39   49    1
   41   44    1
   42   44    1
   43   44    1
   44   50    1
   44   52    1
   45   48    1
   45   49    1
   48   50    1
   48   52    1
   54   60    1
   54   61    1
   54   62    1
   57   60    1
   57   61    1
   57   62    1
[ angles ]
;  ai   aj   ak  funct   angle     fc
    1    2    3    2    106.00   848.00
    1    2    4    2    103.00   420.00
    1    2    5    2    102.00   969.00
    3    2    4    2    134.00  2590.00
    3    2    5    2    106.75   503.00
    4    2    5    2    106.75   503.00
    2    5    6    2    118.00  1330.00
    2    5   19    2    113.00   545.00
    6    5   19    2    120.00   560.00
    5    6    7    2    120.00   505.00
    5    6    8    2    120.00   560.00
    7    6    8    2    120.00   505.00
    6    8    9    2    120.00   560.00
    6    8   15    2    120.00   560.00
    9    8   15    2    120.00   560.00
    8    9   10    2    116.00   465.00
    8    9   11    2    124.00   730.00
   10    9   11    2    116.00   465.00
    9   11   12    2    110.00  1270.00
    9   11   13    2    109.60   450.00
    9   11   14    2    107.57   484.00
   12   11   13    2    110.30   524.00
   12   11   14    2    109.60   450.00
   13   11   14    2    110.00  1270.00
    8   15   16    2    120.00   505.00
    8   15   17    2    120.00   560.00
   16   15   17    2    120.00   505.00
   15   17   18    2    120.00   505.00
   15   17   19    2    120.00   560.00
   18   17   19    2    120.00   505.00
    5   19   17    2    111.00   530.00
    5   19   20    2    115.00   610.00
   17   19   20    2    126.00   640.00
   19   20   21    2    109.50   425.00
   19   20   22    2    121.00   685.00
   21   20   22    2    123.00   415.00
   20   22   23    2    120.00   560.00
   20   22   25    2    120.00   560.00
   23   22   25    2    120.00   560.00
   22   23   24    2    120.00   505.00
   22   23   30    2    120.00   560.00
   24   23   30    2    120.00   505.00
   22   25   26    2    120.00   505.00
   22   25   27    2    120.00   560.00
   26   25   27    2    120.00   505.00
   25   27   28    2    120.00   505.00
   25   27   29    2    120.00   560.00
   28   27   29    2    120.00   505.00
   27   29   30    2    120.00   560.00
   27   29   32    2    120.00   560.00
   30   29   32    2    120.00   560.00
   23   30   29    2    120.00   560.00
   23   30   31    2    120.00   505.00
   29   30   31    2    120.00   505.00
   29   32   33    2    109.50   425.00
   29   32   34    2    116.00   620.00
   33   32   34    2    109.50   425.00
   32   34   35    2    120.00   560.00
   32   34   37    2    120.00   560.00
   35   34   37    2    120.00   560.00
   34   35   36    2    120.00   505.00
   34   35   45    2    120.00   560.00
   36   35   45    2    120.00   505.00
   34   37   38    2    120.00   505.00
   34   37   39    2    120.00   560.00
   38   37   39    2    120.00   505.00
   37   39   40    2    118.00  1330.00
   37   39   44    2    120.00   560.00
   40   39   44    2    125.00   750.00
   39   40   41    2    106.75   503.00
   39   40   42    2    106.75   503.00
   39   40   43    2    106.75   503.00
   41   40   42    2    117.20   636.00
   41   40   43    2    109.50   285.00
   42   40   43    2    113.00   545.00
   39   44   45    2    120.00   560.00
   39   44   47    2    120.00   560.00
   45   44   47    2    120.00   560.00
   35   45   44    2    120.00   560.00
   35   45   46    2    120.00   505.00
   44   45   46    2    120.00   505.00
   44   47   48    2    109.50   425.00
   44   47   49    2    121.00   685.00
   48   47   49    2    115.00   460.00
   47   49   50    2    126.00   640.00
   47   49   52    2    115.00   610.00
   50   49   52    2    120.00   560.00
   49   50   51    2    120.00   505.00
   49   50   57    2    120.00   560.00
   51   50   57    2    120.00   505.00
   49   52   53    2    120.00   505.00
   49   52   54    2    120.00   560.00
   53   52   54    2    120.00   505.00
   52   54   55    2    120.00   505.00
   52   54   56    2    120.00   560.00
   55   54   56    2    120.00   505.00
   54   56   57    2    120.00   560.00
   54   56   59    2    120.00   560.00
   57   56   59    2    120.00   560.00
   50   57   56    2    120.00   560.00
   50   57   58    2    120.00   505.00
   56   57   58    2    120.00   505.00
   56   59   60    2    111.00   530.00
   56   59   61    2    111.00   530.00
   56   59   62    2    111.00   530.00
   60   59   61    2    108.00   465.00
   60   59   62    2    108.53   443.00
   61   59   62    2    107.57   484.00
[ dihedrals ]
; GROMOS improper dihedrals
;  ai   aj   ak   al  funct   angle     fc
    8    6    5   19    2      0.00   167.36
    6    5   19   17    2      0.00   167.36
    5   19   17   15    2      0.00   167.36
   19   17   15    8    2      0.00   167.36
   17   15    8    6    2      0.00   167.36
   15    8    6    5    2      0.00   167.36
   22   23   30   29    2      0.00   167.36
   23   30   29   27    2      0.00   167.36
   30   29   27   25    2      0.00   167.36
   29   27   25   22    2      0.00   167.36
   27   25   22   23    2      0.00   167.36
   25   22   23   30    2      0.00   167.36
   34   37   39   44    2      0.00   167.36
   37   39   44   45    2      0.00   167.36
   39   44   45   35    2      0.00   167.36
   44   45   35   34    2      0.00   167.36
   45   35   34   37    2      0.00   167.36
   35   34   37   39    2      0.00   167.36
   49   50   57   56    2      0.00   167.36
   50   57   56   54    2      0.00   167.36
   57   56   54   52    2      0.00   167.36
   56   54   52   49    2      0.00   167.36
   54   52   49   50    2      0.00   167.36
   52   49   50   57    2      0.00   167.36
    9    8   10   11    2      0.00   167.36
    8    6    9   15    2      0.00   167.36
   15    8   16   17    2      0.00   167.36
   17   15   18   19    2      0.00   167.36
   19    5   17   20    2      0.00   167.36
    5    2    6   19    2      0.00   167.36
    6    5    7    8    2      0.00   167.36
   20   19   21   22    2      0.00   167.36
   22   20   23   25    2      0.00   167.36
   23   22   24   30    2      0.00   167.36
   30   23   29   31    2      0.00   167.36
   29   27   30   32    2      0.00   167.36
   27   25   28   29    2      0.00   167.36
   25   22   26   27    2      0.00   167.36
   34   32   35   37    2      0.00   167.36
   35   34   36   45    2      0.00   167.36
   45   35   44   46    2      0.00   167.36
   44   39   45   47    2      0.00   167.36
   39   37   40   44    2      0.00   167.36
   37   34   38   39    2      0.00   167.36
   49   47   50   52    2      0.00   167.36
   52   49   53   54    2      0.00   167.36
   54   52   55   56    2      0.00   167.36
   56   54   57   59    2      0.00   167.36
   57   50   56   58    2      0.00   167.36
   50   49   51   57    2      0.00   167.36
[ dihedrals ]
;  ai   aj   ak   al  funct    ph0      cp     mult
    3    2    5   19    1      0.00     1.00    6
   15    8    9   11    1    180.00    33.50    2
    8    9   11   12    1    180.00     1.00    6
   17   19   20   22    1    180.00    33.50    2
   19   20   22   23    1      0.00     0.42    2
   30   29   32   34    1      0.00     0.42    2
   29   32   34   35    1      0.00     0.42    2
   44   39   40   41    1      0.00     1.00    6
   45   44   47   49    1      0.00     0.42    2
   44   47   49   52    1    180.00    33.50    2
   54   56   59   60    1      0.00     1.00    6
[ exclusions ]
;  ai   aj  funct  ;  GROMOS 1-4 exclusions
    2    7
    2    8
    2   17
    2   20
    5    9
    5   15
    5   18
    6   16
    6   17
    6   20
    7    9
    7   15
    7   19
    8   18
    8   19
    9   16
    9   17
   15   20
   16   18
   16   19
   18   20
   20   24
   20   26
   20   27
   20   30
   22   28
   22   29
   22   31
   23   26
   23   27
   23   32
   24   25
   24   29
   24   31
   25   30
   25   32
   26   28
   26   29
   27   31
   28   30
   28   32
   31   32
   32   36
   32   38
   32   39
   32   45
   34   40
   34   44
   34   46
   35   38
   35   39
   35   47
   36   37
   36   44
   36   46
   37   45
   37   47
   38   40
   38   44
   39   46
   40   45
   40   47
   46   47
   47   51
   47   53
   47   54
   47   57
   49   55
   49   56
   49   58
   50   53
   50   54
   50   59
   51   52
   51   56
   51   58
   52   57
   52   59
   53   55
   53   56
   54   58
   55   57
   55   59
   58   59

Friday, April 24, 2015

A general chemical structure of polyaniline and its repeating units





A general chemical structure of polyaniline and its repeating units.
(a) A general chemical structure of polyaniline,
(b) Reduced repeating unit, and
(c) oxidized repeating unit

Wednesday, April 01, 2015

Does the type of chemical bond (single, double, triple), built by JSME Molecular Editor, directly influence on the final result of ATB builder (http://compbio.biosci.uq.edu.au/atb/), not by number of built protons? 
I built a molecule with a some double bond, number of protons is correct, however finally ATB's "Show structure" option shows this bond as a single bond, however number of protons there as for a double bond. 
Is it an error of visualization only or built topology files have errors?

Sunday, March 15, 2015

Wednesday, March 11, 2015

Toluene Prodgr

The PDB file (all hydrogens)
REMARK  
REMARK  
REMARK  This file was generated by PRODRG version AA100323.0717
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK  
REMARK  Questions/comments to dava@davapc1.bioch.dundee.ac.uk
REMARK  
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK  
REMARK  
HETATM    1  CAG DRG     1      -7.620   3.400   8.770  1.00 20.00           C  
HETATM    2  HAG DRG     1      -6.729   2.808   8.977  1.00 20.00           H  
HETATM    3  HAH DRG     1      -7.326   4.380   8.395  1.00 20.00           H  
HETATM    4  HAI DRG     1      -8.244   3.492   9.659  1.00 20.00           H  
HETATM    5  CAC DRG     1      -8.400   2.750   7.810  1.00 20.00           C  
HETATM    6  CAB DRG     1      -7.960   1.520   7.260  1.00 20.00           C  
HETATM    7  HAB DRG     1      -7.030   1.060   7.600  1.00 20.00           H  
HETATM    8  CAA DRG     1      -8.740   0.870   6.280  1.00 20.00           C  
HETATM    9  HAA DRG     1      -8.410  -0.070   5.850  1.00 20.00           H  
HETATM   10  CAD DRG     1      -9.950   1.460   5.860  1.00 20.00           C  
HETATM   11  HAD DRG     1     -10.550   0.960   5.100  1.00 20.00           H  
HETATM   12  CAE DRG     1     -10.400   2.690   6.400  1.00 20.00           C  
HETATM   13  HAE DRG     1     -11.340   3.130   6.070  1.00 20.00           H  
HETATM   14  CAF DRG     1      -9.620   3.340   7.380  1.00 20.00           C  
HETATM   15  HAF DRG     1      -9.960   4.280   7.800  1.00 20.00           H  
CONECT    1    2    3    4    5
CONECT    2    1
CONECT    3    1
CONECT    4    1
CONECT    5    1    6   14
CONECT    6    5    7    8
CONECT    7    6
CONECT    8    6    9   10
CONECT    9    8
CONECT   10    8   11   12
CONECT   11   10
CONECT   12   10   13   14
CONECT   13   12
CONECT   14    5   12   15
CONECT   15   14
END

The PDB file (polar/aromatic hydrogens)
REMARK  
REMARK  
REMARK  This file was generated by PRODRG version AA100323.0717
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK  
REMARK  Questions/comments to dava@davapc1.bioch.dundee.ac.uk
REMARK  
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK  
REMARK  
HETATM    1  CAG DRG     1      -7.620   3.400   8.770  1.00 20.00           C  
HETATM    2  CAC DRG     1      -8.400   2.750   7.810  1.00 20.00           C  
HETATM    3  CAB DRG     1      -7.960   1.520   7.260  1.00 20.00           C  
HETATM    4  HAB DRG     1      -7.030   1.060   7.600  1.00 20.00           H  
HETATM    5  CAA DRG     1      -8.740   0.870   6.280  1.00 20.00           C  
HETATM    6  HAA DRG     1      -8.410  -0.070   5.850  1.00 20.00           H  
HETATM    7  CAD DRG     1      -9.950   1.460   5.860  1.00 20.00           C  
HETATM    8  HAD DRG     1     -10.550   0.960   5.100  1.00 20.00           H  
HETATM    9  CAE DRG     1     -10.400   2.690   6.400  1.00 20.00           C  
HETATM   10  HAE DRG     1     -11.340   3.130   6.070  1.00 20.00           H  
HETATM   11  CAF DRG     1      -9.620   3.340   7.380  1.00 20.00           C  
HETATM   12  HAF DRG     1      -9.960   4.280   7.800  1.00 20.00           H  
CONECT    1    2
CONECT    2    1    3   11
CONECT    3    2    4    5
CONECT    4    3
CONECT    5    3    6    7
CONECT    6    5
CONECT    7    5    8    9
CONECT    8    7
CONECT    9    7   10   11
CONECT   10    9
CONECT   11    2    9   12
CONECT   12   11
END


The PDB file (polar hydrogens)
REMARK  
REMARK  
REMARK  This file was generated by PRODRG version AA100323.0717
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK  
REMARK  Questions/comments to dava@davapc1.bioch.dundee.ac.uk
REMARK  
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK  
REMARK  
HETATM    1  CAG DRG     1      -7.620   3.400   8.770  1.00 20.00           C  
HETATM    2  CAC DRG     1      -8.400   2.750   7.810  1.00 20.00           C  
HETATM    3  CAB DRG     1      -7.960   1.520   7.260  1.00 20.00           C  
HETATM    4  CAA DRG     1      -8.740   0.870   6.280  1.00 20.00           C  
HETATM    5  CAD DRG     1      -9.950   1.460   5.860  1.00 20.00           C  
HETATM    6  CAE DRG     1     -10.400   2.690   6.400  1.00 20.00           C  
HETATM    7  CAF DRG     1      -9.620   3.340   7.380  1.00 20.00           C  
CONECT    1    2
CONECT    2    1    3    7
CONECT    3    2    4
CONECT    4    3    5
CONECT    5    4    6
CONECT    6    5    7
CONECT    7    2    6
END


The PDB file (no hydrogens)
REMARK  
REMARK  
REMARK  This file was generated by PRODRG version AA100323.0717
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK  
REMARK  Questions/comments to dava@davapc1.bioch.dundee.ac.uk
REMARK  
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK  
REMARK  
HETATM    1  CAG DRG     1      -7.620   3.400   8.770  1.00 20.00           C  
HETATM    2  CAC DRG     1      -8.400   2.750   7.810  1.00 20.00           C  
HETATM    3  CAB DRG     1      -7.960   1.520   7.260  1.00 20.00           C  
HETATM    4  CAA DRG     1      -8.740   0.870   6.280  1.00 20.00           C  
HETATM    5  CAD DRG     1      -9.950   1.460   5.860  1.00 20.00           C  
HETATM    6  CAE DRG     1     -10.400   2.690   6.400  1.00 20.00           C  
HETATM    7  CAF DRG     1      -9.620   3.340   7.380  1.00 20.00           C  
CONECT    1    2
CONECT    2    1    3    7
CONECT    3    2    4
CONECT    4    3    5
CONECT    5    4    6
CONECT    6    5    7
CONECT    7    2    6
END

The GROMACS topology
;       
;       
;       This file was generated by PRODRG version AA100323.0717
;       PRODRG written/copyrighted by Daan van Aalten
;       and Alexander Schuettelkopf
;       
;       Questions/comments to dava@davapc1.bioch.dundee.ac.uk
;       
;       When using this software in a publication, cite:
;       A. W. Schuettelkopf and D. M. F. van Aalten (2004).
;       PRODRG - a tool for high-throughput crystallography
;       of protein-ligand complexes.
;       Acta Crystallogr. D60, 1355--1363.
;       
;       

[ moleculetype ]
; Name nrexcl
DRG      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CH3     1  DRG     CAG     1    0.040  15.0350   
     2         C     1  DRG     CAC     1   -0.020  12.0110   
     3       CR1     1  DRG     CAB     1   -0.012  12.0110   
     4        HC     1  DRG     HAB     1    0.008   1.0080   
     5       CR1     1  DRG     CAA     1   -0.012  12.0110   
     6        HC     1  DRG     HAA     1    0.008   1.0080   
     7       CR1     1  DRG     CAD     1   -0.012  12.0110   
     8        HC     1  DRG     HAD     1    0.008   1.0080   
     9       CR1     1  DRG     CAE     1   -0.012  12.0110   
    10        HC     1  DRG     HAE     1    0.008   1.0080   
    11       CR1     1  DRG     CAF     1   -0.012  12.0110   
    12        HC     1  DRG     HAF     1    0.008   1.0080   

[ bonds ]
; ai  aj  fu    c0, c1, ...
   2   1   2    0.139   8660000.0    0.139   8660000.0 ;   CAC  CAG   
   2   3   2    0.139  10800000.0    0.139  10800000.0 ;   CAC  CAB   
   2  11   2    0.139  10800000.0    0.139  10800000.0 ;   CAC  CAF   
   3   4   2    0.109  12300000.0    0.109  12300000.0 ;   CAB  HAB   
   3   5   2    0.139  10800000.0    0.139  10800000.0 ;   CAB  CAA   
   5   6   2    0.109  12300000.0    0.109  12300000.0 ;   CAA  HAA   
   5   7   2    0.139  10800000.0    0.139  10800000.0 ;   CAA  CAD   
   7   8   2    0.109  12300000.0    0.109  12300000.0 ;   CAD  HAD   
   7   9   2    0.139  10800000.0    0.139  10800000.0 ;   CAD  CAE   
   9  10   2    0.109  12300000.0    0.109  12300000.0 ;   CAE  HAE   
   9  11   2    0.139  10800000.0    0.139  10800000.0 ;   CAE  CAF   
  11  12   2    0.109  12300000.0    0.109  12300000.0 ;   CAF  HAF   

[ pairs ]
; ai  aj  fu    c0, c1, ...
   1   4   1                                           ;   CAG  HAB   
   1   5   1                                           ;   CAG  CAA   
   1   9   1                                           ;   CAG  CAE   
   1  12   1                                           ;   CAG  HAF   
   2   6   1                                           ;   CAC  HAA   
   2   7   1                                           ;   CAC  CAD   
   2  10   1                                           ;   CAC  HAE   
   3   8   1                                           ;   CAB  HAD   
   3   9   1                                           ;   CAB  CAE   
   3  12   1                                           ;   CAB  HAF   
   4   6   1                                           ;   HAB  HAA   
   4   7   1                                           ;   HAB  CAD   
   4  11   1                                           ;   HAB  CAF   
   5  10   1                                           ;   CAA  HAE   
   5  11   1                                           ;   CAA  CAF   
   6   8   1                                           ;   HAA  HAD   
   6   9   1                                           ;   HAA  CAE   
   7  12   1                                           ;   CAD  HAF   
   8  10   1                                           ;   HAD  HAE   
   8  11   1                                           ;   HAD  CAF   
  10  12   1                                           ;   HAE  HAF   

[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   2    120.0       560.0    120.0       560.0 ;   CAG  CAC  CAB   
   1   2  11   2    120.0       560.0    120.0       560.0 ;   CAG  CAC  CAF   
   3   2  11   2    120.0       560.0    120.0       560.0 ;   CAB  CAC  CAF   
   2   3   4   2    120.0       505.0    120.0       505.0 ;   CAC  CAB  HAB   
   2   3   5   2    120.0       505.0    120.0       505.0 ;   CAC  CAB  CAA   
   4   3   5   2    120.0       505.0    120.0       505.0 ;   HAB  CAB  CAA   
   3   5   6   2    120.0       505.0    120.0       505.0 ;   CAB  CAA  HAA   
   3   5   7   2    120.0       505.0    120.0       505.0 ;   CAB  CAA  CAD   
   6   5   7   2    120.0       505.0    120.0       505.0 ;   HAA  CAA  CAD   
   5   7   8   2    120.0       505.0    120.0       505.0 ;   CAA  CAD  HAD   
   5   7   9   2    120.0       505.0    120.0       505.0 ;   CAA  CAD  CAE   
   8   7   9   2    120.0       505.0    120.0       505.0 ;   HAD  CAD  CAE   
   7   9  10   2    120.0       505.0    120.0       505.0 ;   CAD  CAE  HAE   
   7   9  11   2    120.0       505.0    120.0       505.0 ;   CAD  CAE  CAF   
  10   9  11   2    120.0       505.0    120.0       505.0 ;   HAE  CAE  CAF   
   2  11   9   2    120.0       505.0    120.0       505.0 ;   CAC  CAF  CAE   
   2  11  12   2    120.0       505.0    120.0       505.0 ;   CAC  CAF  HAF   
   9  11  12   2    120.0       505.0    120.0       505.0 ;   CAE  CAF  HAF   

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
   2   1  11   3   2      0.0  167.4        0.0  167.4   ; imp   CAC  CAG  CAF  CAB   
   3   2   5   4   2      0.0  167.4        0.0  167.4   ; imp   CAB  CAC  CAA  HAB   
   5   3   7   6   2      0.0  167.4        0.0  167.4   ; imp   CAA  CAB  CAD  HAA   
   7   5   9   8   2      0.0  167.4        0.0  167.4   ; imp   CAD  CAA  CAE  HAD   
   9   7  11  10   2      0.0  167.4        0.0  167.4   ; imp   CAE  CAD  CAF  HAE   
  11   2   9  12   2      0.0  167.4        0.0  167.4   ; imp   CAF  CAC  CAE  HAF   
   2   3   5   7   2      0.0  209.3        0.0  209.3   ; imp   CAC  CAB  CAA  CAD   
   3   5   7   9   2      0.0  209.3        0.0  209.3   ; imp   CAB  CAA  CAD  CAE   
   5   7   9  11   2      0.0  209.3        0.0  209.3   ; imp   CAA  CAD  CAE  CAF   
   7   9  11   2   2      0.0  209.3        0.0  209.3   ; imp   CAD  CAE  CAF  CAC   
   9  11   2   3   2      0.0  209.3        0.0  209.3   ; imp   CAE  CAF  CAC  CAB   
  11   2   3   5   2      0.0  209.3        0.0  209.3   ; imp   CAF  CAC  CAB  CAA   


Tetra(analine)

tetra(aniline)_5LDA_GROMOS96_allatom_optimised_geometry


Friday, March 06, 2015

Steps to Perform a Simulation

Below is presented a generalised procedure for performing a simulation. The exact steps and processes involved will vary depending on exactly what is being attempted. Use as a general guide only!

  1. Clearly identify the property / phenomena of interest to be studied by performing the simulation. Do not continue further until you are clear on this!
  2. Select the appropriate tools to be able to perform the simulation and observe the property / phenomena of interest. It is important to read and familiarise yourself with publications by other researchers on similar systems. Tools include:

    - software to perform the simulation with, consideration of force field may influence this decision.

    force field which describes how the atoms / particles within the system interact with each other. Select one that is appropriate for the system being studied and the property / phenomena of interest. Very important and non-trivial step! Consider now how you will analyze your simulation data to make your observations.
  3. Obtain / generate the initial coordinate file for each molecule to be placed within the system. The page linked there has some software suggestions.
  4. Generate the raw starting structure for the system by placing the molecules within the coordinate file as appropriate. Molecules may be specifically placed or arranged randomly.
  5. Obtain / generate the topology file for the system, using (for example)
    pdb2gmx
    SwissParam (for CHARMM forcefield), 
    PRODRG (for ffgmx/GROMOS96 43A1), 
    Automated Topology Builder (for GROMOS96 53A6), 
    MKTOP (for OPLS/AA) or
    - your favourite text editor in concert with chapter 5 of the
    GROMACS Manual.
    - For the 
    AMBER force fields, antechamber or acpype might be appropriate.
  6. Describe a simulation box (e.g. using editconf) whose size is appropriate for the eventual density you would like, fill it with solvent (e.g. using genbox), and add any counter-ions needed to neutralize the system (e.g. using grompp and genion). In these steps you may need to edit your topology file to stay current with your coordinate file.
  7. Run an energy minimization on the system (using grompp and mdrun). This is required to sort out any bad starting structures caused during generation of the system, which may cause the production simulation to crash. It may be necessary also to minimize your solute structure in vacuo before introducing solvent molecules (or your lipid bilayer or whatever else). You should consider using flexible water models and not using bond constraints or frozen groups. The use of position restraints and/or distance restraints should be evaluated carefully.
  8. Select the appropriate simulation parameters for the equilibration simulation (defined in .mdp file). You need to choose simulation parameters that are consistent with how force field was derived. You may need to simulate at NVT with position restraints on your solvent and/or solute to get the temperature almost right, then relax to NPT to fix the density (which should be done with Berendsen until after the density is stabilized, before a further switch to a barostat that produces the correct ensemble), then move further (if needed) to reach your production simulation ensemble (e.g. NVTNVE). If you have problems here with the system blowing up, consider using the suggestions on that page, e.g. position restraints on solutes, or not using bond constraints, or using smaller integration timesteps, or several gentler heating stage(s).
  9. Run the equilibration simulation for sufficient time so that the system relaxes sufficiently in the target ensemble to allow the production run to be commenced (using grompp and mdrun, then g_energy and trajectory visualization tools).
  10. Select the appropriate simulation parameters for the production simulation (defined in .mdp file). In particular, be careful not to re-generate the velocities. You still need to be consistent with how the force field was derived and how to measure the property / phenomena of interest.
  11. Run the production simulation for sufficient time so that property / phenomena of interest can be observed in required detail (using grompp / tpbconv and mdrun).
  12. Analyse / visualise the resulting trajectory and data files to obtain information on the property / phenomena of interest.

Thursday, March 05, 2015

Fatal error: Atomtype SDMSO not found

Fatal error:
Atomtype SDMSO not found

Error was deleted by changing SDMSO into SDmso in the itp file, obtained from the site of topology calculation PRODRG.

25     SDMSO     1  AMO     SAB     6    1.652  32.0600 

topol.top

;
; File 'topol.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Wed Mar 04 23:33:55 2015
;
; This is your topology file
; "Torture You.... Yeah, That's a Good Idea, I Like That." (Pulp Fiction)
;
; Include forcefield parameters
#include "ffG43a1.itp"
#include "AMO.ITP"

[ system ]
AMO 4

[ molecules ]
AMO 4

AMO.itp

;       
;       
;       This file was generated by PRODRG version AA100323.0717
;       PRODRG written/copyrighted by Daan van Aalten
;       and Alexander Schuettelkopf
;       
;       Questions/comments to dava@davapc1.bioch.dundee.ac.uk
;       
;       When using this software in a publication, cite:
;       A. W. Schuettelkopf and D. M. F. van Aalten (2004).
;       PRODRG - a tool for high-throughput crystallography
;       of protein-ligand complexes.
;       Acta Crystallogr. D60, 1355--1363.
;       
;       

[ moleculetype ]
; Name nrexcl
AMO      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CH3     1  AMO     CBE     1   -0.011  15.0350   
     2       CH2     1  AMO     CBD     1    0.011  14.0270   
     3       CH2     1  AMO     CBC     2    0.000  14.0270   
     4       CH2     1  AMO     CBB     2    0.000  14.0270   
     5       CH2     1  AMO     CBA     2    0.001  14.0270   
     6       CH2     1  AMO     CAZ     2   -0.001  14.0270   
     7       CH2     1  AMO     CAY     3    0.000  14.0270   
     8       CH2     1  AMO     CAX     3    0.002  14.0270   
     9       CH2     1  AMO     CAW     3    0.000  14.0270   
    10       CH2     1  AMO     CAV     3    0.000  14.0270   
    11       CH2     1  AMO     CAU     3    0.000  14.0270   
    12       CH2     1  AMO     CAT     3   -0.001  14.0270   
    13       CH2     1  AMO     CAS     3   -0.001  14.0270   
    14       CH2     1  AMO     CAR     4    0.037  14.0270   
    15       CH2     1  AMO     CAQ     4    0.038  14.0270   
    16       CH2     1  AMO     CAP     4    0.038  14.0270   
    17       CH2     1  AMO     CAO     4    0.036  14.0270   
    18       CH2     1  AMO     CAN     4    0.038  14.0270   
    19         C     1  AMO     CAL     4    0.219  12.0110   
    20         O     1  AMO     OAM     4   -0.406  15.9994   
    21         C     1  AMO     CAJ     5   -0.002  12.0110   
    22       CR1     1  AMO     CAK     5   -0.002  12.0110   
    23        HC     1  AMO     HAK     5    0.006   1.0080   
    24         C     1  AMO     CAE     5   -0.002  12.0110   
    25     SDMSO     1  AMO     SAB     6    1.652  32.0600   
    26        OM     1  AMO     OAC     6   -0.569  15.9994   
    27        OM     1  AMO     OAD     6   -0.569  15.9994   
    28        OM     1  AMO     OAA     6   -0.569  15.9994   
    29       CR1     1  AMO     CAI     6   -0.015  12.0110   
    30        HC     1  AMO     HAI     6    0.001   1.0080   
    31       CR1     1  AMO     CAG     6   -0.016  12.0110   
    32        HC     1  AMO     HAG     6    0.001   1.0080   
    33         C     1  AMO     CAF     6    0.084  12.0110   
    34         N     1  AMO     NAH     7    0.032  14.0067   
    35         H     1  AMO     HAH     7   -0.027   1.0080   
    36         C     1  AMO     CBF     7    0.032  12.0110   
    37       CR1     1  AMO     CBJ     7   -0.037  12.0110   
    38        HC     1  AMO     HBQ     7    0.000   1.0080   
    39       CR1     1  AMO     CBK     8   -0.021  12.0110   
    40        HC     1  AMO     HBR     8    0.001   1.0080   
    41       CR1     1  AMO     CBG     8   -0.020  12.0110   
    42        HC     1  AMO     HBO     8    0.000   1.0080   
    43       CR1     1  AMO     CBH     8   -0.021  12.0110   
    44        HC     1  AMO     HBP     8    0.001   1.0080   
    45         C     1  AMO     CBI     8    0.060  12.0110   
    46         N     1  AMO     NBL     9    0.044  14.0067   
    47         H     1  AMO     HBZ     9   -0.020   1.0080   
    48         C     1  AMO     CBM     9    0.044  12.0110   
    49       CR1     1  AMO     CBO     9   -0.028  12.0110   
    50        HC     1  AMO     HBT     9    0.000   1.0080   
    51         C     1  AMO     CBP     9   -0.040  12.0110   
    52     SDMSO     1  AMO     SCA    10    1.652  32.0600   
    53        OM     1  AMO     OCC    10   -0.569  15.9994   
    54        OM     1  AMO     OCD    10   -0.569  15.9994   
    55        OM     1  AMO     OCB    10   -0.569  15.9994   
    56       CR1     1  AMO     CBN    10   -0.015  12.0110   
    57        HC     1  AMO     HBS    10    0.001   1.0080   
    58       CR1     1  AMO     CBR    10   -0.016  12.0110   
    59        HC     1  AMO     HBU    10    0.001   1.0080   
    60         C     1  AMO     CBQ    10    0.084  12.0110   
    61         N     1  AMO     NBS    11    0.032  14.0067   
    62         H     1  AMO     HB0    11   -0.027   1.0080   
    63         C     1  AMO     CBT    11    0.032  12.0110   
    64       CR1     1  AMO     CBU    11   -0.037  12.0110   
    65        HC     1  AMO     HBV    11    0.000   1.0080   
    66       CR1     1  AMO     CBV    12   -0.019  12.0110   
    67        HC     1  AMO     HBW    12    0.001   1.0080   
    68         C     1  AMO     CBW    12    0.064  12.0110   
    69        NT     1  AMO     NBZ    12    0.019  14.0067   
    70         H     1  AMO     HB2    12   -0.014   1.0080   
    71         H     1  AMO     HB1    12   -0.014   1.0080   
    72       CR1     1  AMO     CBY    12   -0.020  12.0110   
    73        HC     1  AMO     HBY    12    0.001   1.0080   
    74       CR1     1  AMO     CBX    12   -0.019  12.0110   
    75        HC     1  AMO     HBX    12    0.001   1.0080   

[ bonds ]
; ai  aj  fu    c0, c1, ...
   2   1   2    0.153   7150000.0    0.153   7150000.0 ;   CBD  CBE   
   2   3   2    0.153   7150000.0    0.153   7150000.0 ;   CBD  CBC   
   3   4   2    0.153   7150000.0    0.153   7150000.0 ;   CBC  CBB   
   4   5   2    0.153   7150000.0    0.153   7150000.0 ;   CBB  CBA   
   5   6   2    0.153   7150000.0    0.153   7150000.0 ;   CBA  CAZ   
   6   7   2    0.153   7150000.0    0.153   7150000.0 ;   CAZ  CAY   
   7   8   2    0.153   7150000.0    0.153   7150000.0 ;   CAY  CAX   
   8   9   2    0.153   7150000.0    0.153   7150000.0 ;   CAX  CAW   
   9  10   2    0.153   7150000.0    0.153   7150000.0 ;   CAW  CAV   
  10  11   2    0.153   7150000.0    0.153   7150000.0 ;   CAV  CAU   
  11  12   2    0.153   7150000.0    0.153   7150000.0 ;   CAU  CAT   
  12  13   2    0.153   7150000.0    0.153   7150000.0 ;   CAT  CAS   
  13  14   2    0.153   7150000.0    0.153   7150000.0 ;   CAS  CAR   
  14  15   2    0.153   7150000.0    0.153   7150000.0 ;   CAR  CAQ   
  15  16   2    0.153   7150000.0    0.153   7150000.0 ;   CAQ  CAP   
  16  17   2    0.153   7150000.0    0.153   7150000.0 ;   CAP  CAO   
  17  18   2    0.153   7150000.0    0.153   7150000.0 ;   CAO  CAN   
  19  18   2    0.153   7150000.0    0.153   7150000.0 ;   CAL  CAN   
  19  20   2    0.123  16600000.0    0.123  16600000.0 ;   CAL  OAM   
  21  19   2    0.139  10800000.0    0.139  10800000.0 ;   CAJ  CAL   
  21  22   2    0.139  10800000.0    0.139  10800000.0 ;   CAJ  CAK   
  21  29   2    0.139  10800000.0    0.139  10800000.0 ;   CAJ  CAI   
  22  23   2    0.109  12300000.0    0.109  12300000.0 ;   CAK  HAK   
  24  22   2    0.139  10800000.0    0.139  10800000.0 ;   CAE  CAK   
  24  25   2    0.175   2619184.0    0.175   2619184.0 ;   CAE  SAB   
  24  33   2    0.139  10800000.0    0.139  10800000.0 ;   CAE  CAF   
  25  26   2    0.153   8040000.0    0.153   8040000.0 ;   SAB  OAC   
  25  27   2    0.153   8040000.0    0.153   8040000.0 ;   SAB  OAD   
  25  28   2    0.153   8040000.0    0.153   8040000.0 ;   SAB  OAA   
  29  30   2    0.109  12300000.0    0.109  12300000.0 ;   CAI  HAI   
  29  31   2    0.139  10800000.0    0.139  10800000.0 ;   CAI  CAG   
  31  32   2    0.109  12300000.0    0.109  12300000.0 ;   CAG  HAG   
  33  31   2    0.139  10800000.0    0.139  10800000.0 ;   CAF  CAG   
  33  34   2    0.133  10600000.0    0.133  10600000.0 ;   CAF  NAH   
  34  35   2    0.100  18700000.0    0.100  18700000.0 ;   NAH  HAH   
  36  34   2    0.133  10600000.0    0.133  10600000.0 ;   CBF  NAH   
  36  37   2    0.139  10800000.0    0.139  10800000.0 ;   CBF  CBJ   
  36  41   2    0.139  10800000.0    0.139  10800000.0 ;   CBF  CBG   
  37  38   2    0.109  12300000.0    0.109  12300000.0 ;   CBJ  HBQ   
  37  39   2    0.139  10800000.0    0.139  10800000.0 ;   CBJ  CBK   
  39  40   2    0.109  12300000.0    0.109  12300000.0 ;   CBK  HBR   
  45  39   2    0.139  10800000.0    0.139  10800000.0 ;   CBI  CBK   
  41  42   2    0.109  12300000.0    0.109  12300000.0 ;   CBG  HBO   
  41  43   2    0.139  10800000.0    0.139  10800000.0 ;   CBG  CBH   
  43  44   2    0.109  12300000.0    0.109  12300000.0 ;   CBH  HBP   
  45  43   2    0.139  10800000.0    0.139  10800000.0 ;   CBI  CBH   
  45  46   2    0.133  10600000.0    0.133  10600000.0 ;   CBI  NBL   
  46  47   2    0.100  18700000.0    0.100  18700000.0 ;   NBL  HBZ   
  48  46   2    0.133  10600000.0    0.133  10600000.0 ;   CBM  NBL   
  48  49   2    0.139  10800000.0    0.139  10800000.0 ;   CBM  CBO   
  48  56   2    0.139  10800000.0    0.139  10800000.0 ;   CBM  CBN   
  49  50   2    0.109  12300000.0    0.109  12300000.0 ;   CBO  HBT   
  51  49   2    0.139  10800000.0    0.139  10800000.0 ;   CBP  CBO   
  51  52   2    0.175   2619184.0    0.175   2619184.0 ;   CBP  SCA   
  51  60   2    0.139  10800000.0    0.139  10800000.0 ;   CBP  CBQ   
  52  53   2    0.153   8040000.0    0.153   8040000.0 ;   SCA  OCC   
  52  54   2    0.153   8040000.0    0.153   8040000.0 ;   SCA  OCD   
  52  55   2    0.153   8040000.0    0.153   8040000.0 ;   SCA  OCB   
  56  57   2    0.109  12300000.0    0.109  12300000.0 ;   CBN  HBS   
  56  58   2    0.139  10800000.0    0.139  10800000.0 ;   CBN  CBR   
  58  59   2    0.109  12300000.0    0.109  12300000.0 ;   CBR  HBU   
  60  58   2    0.139  10800000.0    0.139  10800000.0 ;   CBQ  CBR   
  60  61   2    0.133  10600000.0    0.133  10600000.0 ;   CBQ  NBS   
  61  62   2    0.100  18700000.0    0.100  18700000.0 ;   NBS  HB0   
  63  61   2    0.133  10600000.0    0.133  10600000.0 ;   CBT  NBS   
  63  64   2    0.139  10800000.0    0.139  10800000.0 ;   CBT  CBU   
  63  74   2    0.139  10800000.0    0.139  10800000.0 ;   CBT  CBX   
  64  65   2    0.109  12300000.0    0.109  12300000.0 ;   CBU  HBV   
  64  66   2    0.139  10800000.0    0.139  10800000.0 ;   CBU  CBV   
  66  67   2    0.109  12300000.0    0.109  12300000.0 ;   CBV  HBW   
  68  66   2    0.139  10800000.0    0.139  10800000.0 ;   CBW  CBV   
  68  69   2    0.133  10600000.0    0.133  10600000.0 ;   CBW  NBZ   
  68  72   2    0.139  10800000.0    0.139  10800000.0 ;   CBW  CBY   
  69  70   2    0.100  18700000.0    0.100  18700000.0 ;   NBZ  HB2   
  69  71   2    0.100  18700000.0    0.100  18700000.0 ;   NBZ  HB1   
  72  73   2    0.109  12300000.0    0.109  12300000.0 ;   CBY  HBY   
  72  74   2    0.139  10800000.0    0.139  10800000.0 ;   CBY  CBX   
  74  75   2    0.109  12300000.0    0.109  12300000.0 ;   CBX  HBX   

[ pairs ]
; ai  aj  fu    c0, c1, ...
   1   4   1                                           ;   CBE  CBB   
   2   5   1                                           ;   CBD  CBA   
   3   6   1                                           ;   CBC  CAZ   
   4   7   1                                           ;   CBB  CAY   
   5   8   1                                           ;   CBA  CAX   
   6   9   1                                           ;   CAZ  CAW   
   7  10   1                                           ;   CAY  CAV   
   8  11   1                                           ;   CAX  CAU   
   9  12   1                                           ;   CAW  CAT   
  10  13   1                                           ;   CAV  CAS   
  11  14   1                                           ;   CAU  CAR   
  12  15   1                                           ;   CAT  CAQ   
  13  16   1                                           ;   CAS  CAP   
  14  17   1                                           ;   CAR  CAO   
  15  18   1                                           ;   CAQ  CAN   
  16  19   1                                           ;   CAP  CAL   
  17  20   1                                           ;   CAO  OAM   
  17  21   1                                           ;   CAO  CAJ   
  18  22   1                                           ;   CAN  CAK   
  18  29   1                                           ;   CAN  CAI   
  19  23   1                                           ;   CAL  HAK   
  19  24   1                                           ;   CAL  CAE   
  19  30   1                                           ;   CAL  HAI   
  19  31   1                                           ;   CAL  CAG   
  20  22   1                                           ;   OAM  CAK   
  20  29   1                                           ;   OAM  CAI   
  21  25   1                                           ;   CAJ  SAB   
  21  32   1                                           ;   CAJ  HAG   
  21  33   1                                           ;   CAJ  CAF   
  22  26   1                                           ;   CAK  OAC   
  22  27   1                                           ;   CAK  OAD   
  22  28   1                                           ;   CAK  OAA   
  22  30   1                                           ;   CAK  HAI   
  22  31   1                                           ;   CAK  CAG   
  22  34   1                                           ;   CAK  NAH   
  23  25   1                                           ;   HAK  SAB   
  23  29   1                                           ;   HAK  CAI   
  23  33   1                                           ;   HAK  CAF   
  24  29   1                                           ;   CAE  CAI   
  24  32   1                                           ;   CAE  HAG   
  24  35   1                                           ;   CAE  HAH   
  24  36   1                                           ;   CAE  CBF   
  25  31   1                                           ;   SAB  CAG   
  25  34   1                                           ;   SAB  NAH   
  26  33   1                                           ;   OAC  CAF   
  27  33   1                                           ;   OAD  CAF   
  28  33   1                                           ;   OAA  CAF   
  29  34   1                                           ;   CAI  NAH   
  30  32   1                                           ;   HAI  HAG   
  30  33   1                                           ;   HAI  CAF   
  31  35   1                                           ;   CAG  HAH   
  31  36   1                                           ;   CAG  CBF   
  32  34   1                                           ;   HAG  NAH   
  33  37   1                                           ;   CAF  CBJ   
  33  41   1                                           ;   CAF  CBG   
  34  38   1                                           ;   NAH  HBQ   
  34  39   1                                           ;   NAH  CBK   
  34  42   1                                           ;   NAH  HBO   
  34  43   1                                           ;   NAH  CBH   
  35  37   1                                           ;   HAH  CBJ   
  35  41   1                                           ;   HAH  CBG   
  36  40   1                                           ;   CBF  HBR   
  36  44   1                                           ;   CBF  HBP   
  36  45   1                                           ;   CBF  CBI   
  37  42   1                                           ;   CBJ  HBO   
  37  43   1                                           ;   CBJ  CBH   
  37  46   1                                           ;   CBJ  NBL   
  38  40   1                                           ;   HBQ  HBR   
  38  41   1                                           ;   HBQ  CBG   
  38  45   1                                           ;   HBQ  CBI   
  39  41   1                                           ;   CBK  CBG   
  39  44   1                                           ;   CBK  HBP   
  39  47   1                                           ;   CBK  HBZ   
  39  48   1                                           ;   CBK  CBM   
  40  43   1                                           ;   HBR  CBH   
  40  46   1                                           ;   HBR  NBL   
  41  46   1                                           ;   CBG  NBL   
  42  44   1                                           ;   HBO  HBP   
  42  45   1                                           ;   HBO  CBI   
  43  47   1                                           ;   CBH  HBZ   
  43  48   1                                           ;   CBH  CBM   
  44  46   1                                           ;   HBP  NBL   
  45  49   1                                           ;   CBI  CBO   
  45  56   1                                           ;   CBI  CBN   
  46  50   1                                           ;   NBL  HBT   
  46  51   1                                           ;   NBL  CBP   
  46  57   1                                           ;   NBL  HBS   
  46  58   1                                           ;   NBL  CBR   
  47  49   1                                           ;   HBZ  CBO   
  47  56   1                                           ;   HBZ  CBN   
  48  52   1                                           ;   CBM  SCA   
  48  59   1                                           ;   CBM  HBU   
  48  60   1                                           ;   CBM  CBQ   
  49  53   1                                           ;   CBO  OCC   
  49  54   1                                           ;   CBO  OCD   
  49  55   1                                           ;   CBO  OCB   
  49  57   1                                           ;   CBO  HBS   
  49  58   1                                           ;   CBO  CBR   
  49  61   1                                           ;   CBO  NBS   
  50  52   1                                           ;   HBT  SCA   
  50  56   1                                           ;   HBT  CBN   
  50  60   1                                           ;   HBT  CBQ   
  51  56   1                                           ;   CBP  CBN   
  51  59   1                                           ;   CBP  HBU   
  51  62   1                                           ;   CBP  HB0   
  51  63   1                                           ;   CBP  CBT   
  52  58   1                                           ;   SCA  CBR   
  52  61   1                                           ;   SCA  NBS   
  53  60   1                                           ;   OCC  CBQ   
  54  60   1                                           ;   OCD  CBQ   
  55  60   1                                           ;   OCB  CBQ   
  56  61   1                                           ;   CBN  NBS   
  57  59   1                                           ;   HBS  HBU   
  57  60   1                                           ;   HBS  CBQ   
  58  62   1                                           ;   CBR  HB0   
  58  63   1                                           ;   CBR  CBT   
  59  61   1                                           ;   HBU  NBS   
  60  64   1                                           ;   CBQ  CBU   
  60  74   1                                           ;   CBQ  CBX   
  61  65   1                                           ;   NBS  HBV   
  61  66   1                                           ;   NBS  CBV   
  61  72   1                                           ;   NBS  CBY   
  61  75   1                                           ;   NBS  HBX   
  62  64   1                                           ;   HB0  CBU   
  62  74   1                                           ;   HB0  CBX   
  63  67   1                                           ;   CBT  HBW   
  63  68   1                                           ;   CBT  CBW   
  63  73   1                                           ;   CBT  HBY   
  64  69   1                                           ;   CBU  NBZ   
  64  72   1                                           ;   CBU  CBY   
  64  75   1                                           ;   CBU  HBX   
  65  67   1                                           ;   HBV  HBW   
  65  68   1                                           ;   HBV  CBW   
  65  74   1                                           ;   HBV  CBX   
  66  70   1                                           ;   CBV  HB2   
  66  71   1                                           ;   CBV  HB1   
  66  73   1                                           ;   CBV  HBY   
  66  74   1                                           ;   CBV  CBX   
  67  69   1                                           ;   HBW  NBZ   
  67  72   1                                           ;   HBW  CBY   
  68  75   1                                           ;   CBW  HBX   
  69  73   1                                           ;   NBZ  HBY   
  69  74   1                                           ;   NBZ  CBX   
  70  72   1                                           ;   HB2  CBY   
  71  72   1                                           ;   HB1  CBY   
  73  75   1                                           ;   HBY  HBX   

[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   2    109.5       520.0    109.5       520.0 ;   CBE  CBD  CBC   
   2   3   4   2    109.5       520.0    109.5       520.0 ;   CBD  CBC  CBB   
   3   4   5   2    109.5       520.0    109.5       520.0 ;   CBC  CBB  CBA   
   4   5   6   2    109.5       520.0    109.5       520.0 ;   CBB  CBA  CAZ   
   5   6   7   2    109.5       520.0    109.5       520.0 ;   CBA  CAZ  CAY   
   6   7   8   2    109.5       520.0    109.5       520.0 ;   CAZ  CAY  CAX   
   7   8   9   2    109.5       520.0    109.5       520.0 ;   CAY  CAX  CAW   
   8   9  10   2    109.5       520.0    109.5       520.0 ;   CAX  CAW  CAV   
   9  10  11   2    109.5       520.0    109.5       520.0 ;   CAW  CAV  CAU   
  10  11  12   2    109.5       520.0    109.5       520.0 ;   CAV  CAU  CAT   
  11  12  13   2    109.5       520.0    109.5       520.0 ;   CAU  CAT  CAS   
  12  13  14   2    109.5       520.0    109.5       520.0 ;   CAT  CAS  CAR   
  13  14  15   2    109.5       520.0    109.5       520.0 ;   CAS  CAR  CAQ   
  14  15  16   2    109.5       520.0    109.5       520.0 ;   CAR  CAQ  CAP   
  15  16  17   2    109.5       520.0    109.5       520.0 ;   CAQ  CAP  CAO   
  16  17  18   2    109.5       520.0    109.5       520.0 ;   CAP  CAO  CAN   
  17  18  19   2    109.5       520.0    109.5       520.0 ;   CAO  CAN  CAL   
  18  19  20   2    121.0       685.0    121.0       685.0 ;   CAN  CAL  OAM   
  18  19  21   2    115.0       610.0    115.0       610.0 ;   CAN  CAL  CAJ   
  20  19  21   2    121.0       685.0    121.0       685.0 ;   OAM  CAL  CAJ   
  19  21  22   2    120.0       560.0    120.0       560.0 ;   CAL  CAJ  CAK   
  19  21  29   2    120.0       560.0    120.0       560.0 ;   CAL  CAJ  CAI   
  22  21  29   2    120.0       560.0    120.0       560.0 ;   CAK  CAJ  CAI   
  21  22  23   2    120.0       505.0    120.0       505.0 ;   CAJ  CAK  HAK   
  21  22  24   2    120.0       505.0    120.0       505.0 ;   CAJ  CAK  CAE   
  23  22  24   2    120.0       505.0    120.0       505.0 ;   HAK  CAK  CAE   
  22  24  25   2    120.0       560.0    120.0       560.0 ;   CAK  CAE  SAB   
  22  24  33   2    120.0       560.0    120.0       560.0 ;   CAK  CAE  CAF   
  25  24  33   2    120.0       560.0    120.0       560.0 ;   SAB  CAE  CAF   
  24  25  26   2    109.5       518.0    109.5       518.0 ;   CAE  SAB  OAC   
  24  25  27   2    109.5       518.0    109.5       518.0 ;   CAE  SAB  OAD   
  24  25  28   2    109.5       518.0    109.5       518.0 ;   CAE  SAB  OAA   
  26  25  27   2    109.5       518.0    109.5       518.0 ;   OAC  SAB  OAD   
  26  25  28   2    109.5       518.0    109.5       518.0 ;   OAC  SAB  OAA   
  27  25  28   2    109.5       518.0    109.5       518.0 ;   OAD  SAB  OAA   
  21  29  30   2    120.0       505.0    120.0       505.0 ;   CAJ  CAI  HAI   
  21  29  31   2    120.0       505.0    120.0       505.0 ;   CAJ  CAI  CAG   
  30  29  31   2    120.0       505.0    120.0       505.0 ;   HAI  CAI  CAG   
  29  31  32   2    120.0       505.0    120.0       505.0 ;   CAI  CAG  HAG   
  29  31  33   2    120.0       505.0    120.0       505.0 ;   CAI  CAG  CAF   
  32  31  33   2    120.0       505.0    120.0       505.0 ;   HAG  CAG  CAF   
  24  33  31   2    120.0       560.0    120.0       560.0 ;   CAE  CAF  CAG   
  24  33  34   2    115.0       610.0    115.0       610.0 ;   CAE  CAF  NAH   
  31  33  34   2    120.0       560.0    120.0       560.0 ;   CAG  CAF  NAH   
  33  34  35   2    123.0       415.0    123.0       415.0 ;   CAF  NAH  HAH   
  33  34  36   2    117.0       635.0    117.0       635.0 ;   CAF  NAH  CBF   
  35  34  36   2    123.0       415.0    123.0       415.0 ;   HAH  NAH  CBF   
  34  36  37   2    120.0       560.0    120.0       560.0 ;   NAH  CBF  CBJ   
  34  36  41   2    120.0       560.0    120.0       560.0 ;   NAH  CBF  CBG   
  37  36  41   2    120.0       560.0    120.0       560.0 ;   CBJ  CBF  CBG   
  36  37  38   2    120.0       505.0    120.0       505.0 ;   CBF  CBJ  HBQ   
  36  37  39   2    120.0       505.0    120.0       505.0 ;   CBF  CBJ  CBK   
  38  37  39   2    120.0       505.0    120.0       505.0 ;   HBQ  CBJ  CBK   
  37  39  40   2    120.0       505.0    120.0       505.0 ;   CBJ  CBK  HBR   
  37  39  45   2    120.0       505.0    120.0       505.0 ;   CBJ  CBK  CBI   
  40  39  45   2    120.0       505.0    120.0       505.0 ;   HBR  CBK  CBI   
  36  41  42   2    120.0       505.0    120.0       505.0 ;   CBF  CBG  HBO   
  36  41  43   2    120.0       505.0    120.0       505.0 ;   CBF  CBG  CBH   
  42  41  43   2    120.0       505.0    120.0       505.0 ;   HBO  CBG  CBH   
  41  43  44   2    120.0       505.0    120.0       505.0 ;   CBG  CBH  HBP   
  41  43  45   2    120.0       505.0    120.0       505.0 ;   CBG  CBH  CBI   
  44  43  45   2    120.0       505.0    120.0       505.0 ;   HBP  CBH  CBI   
  39  45  43   2    120.0       560.0    120.0       560.0 ;   CBK  CBI  CBH   
  39  45  46   2    120.0       560.0    120.0       560.0 ;   CBK  CBI  NBL   
  43  45  46   2    120.0       560.0    120.0       560.0 ;   CBH  CBI  NBL   
  45  46  47   2    123.0       415.0    123.0       415.0 ;   CBI  NBL  HBZ   
  45  46  48   2    117.0       635.0    117.0       635.0 ;   CBI  NBL  CBM   
  47  46  48   2    123.0       415.0    123.0       415.0 ;   HBZ  NBL  CBM   
  46  48  49   2    120.0       560.0    120.0       560.0 ;   NBL  CBM  CBO   
  46  48  56   2    120.0       560.0    120.0       560.0 ;   NBL  CBM  CBN   
  49  48  56   2    120.0       560.0    120.0       560.0 ;   CBO  CBM  CBN   
  48  49  50   2    120.0       505.0    120.0       505.0 ;   CBM  CBO  HBT   
  48  49  51   2    120.0       505.0    120.0       505.0 ;   CBM  CBO  CBP   
  50  49  51   2    120.0       505.0    120.0       505.0 ;   HBT  CBO  CBP   
  49  51  52   2    120.0       560.0    120.0       560.0 ;   CBO  CBP  SCA   
  49  51  60   2    120.0       560.0    120.0       560.0 ;   CBO  CBP  CBQ   
  52  51  60   2    120.0       560.0    120.0       560.0 ;   SCA  CBP  CBQ   
  51  52  53   2    109.5       518.0    109.5       518.0 ;   CBP  SCA  OCC   
  51  52  54   2    109.5       518.0    109.5       518.0 ;   CBP  SCA  OCD   
  51  52  55   2    109.5       518.0    109.5       518.0 ;   CBP  SCA  OCB   
  53  52  54   2    109.5       518.0    109.5       518.0 ;   OCC  SCA  OCD   
  53  52  55   2    109.5       518.0    109.5       518.0 ;   OCC  SCA  OCB   
  54  52  55   2    109.5       518.0    109.5       518.0 ;   OCD  SCA  OCB   
  48  56  57   2    120.0       505.0    120.0       505.0 ;   CBM  CBN  HBS   
  48  56  58   2    120.0       505.0    120.0       505.0 ;   CBM  CBN  CBR   
  57  56  58   2    120.0       505.0    120.0       505.0 ;   HBS  CBN  CBR   
  56  58  59   2    120.0       505.0    120.0       505.0 ;   CBN  CBR  HBU   
  56  58  60   2    120.0       505.0    120.0       505.0 ;   CBN  CBR  CBQ   
  59  58  60   2    120.0       505.0    120.0       505.0 ;   HBU  CBR  CBQ   
  51  60  58   2    120.0       560.0    120.0       560.0 ;   CBP  CBQ  CBR   
  51  60  61   2    115.0       610.0    115.0       610.0 ;   CBP  CBQ  NBS   
  58  60  61   2    120.0       560.0    120.0       560.0 ;   CBR  CBQ  NBS   
  60  61  62   2    123.0       415.0    123.0       415.0 ;   CBQ  NBS  HB0   
  60  61  63   2    117.0       635.0    117.0       635.0 ;   CBQ  NBS  CBT   
  62  61  63   2    123.0       415.0    123.0       415.0 ;   HB0  NBS  CBT   
  61  63  64   2    120.0       560.0    120.0       560.0 ;   NBS  CBT  CBU   
  61  63  74   2    120.0       560.0    120.0       560.0 ;   NBS  CBT  CBX   
  64  63  74   2    120.0       560.0    120.0       560.0 ;   CBU  CBT  CBX   
  63  64  65   2    120.0       505.0    120.0       505.0 ;   CBT  CBU  HBV   
  63  64  66   2    120.0       505.0    120.0       505.0 ;   CBT  CBU  CBV   
  65  64  66   2    120.0       505.0    120.0       505.0 ;   HBV  CBU  CBV   
  64  66  67   2    120.0       505.0    120.0       505.0 ;   CBU  CBV  HBW   
  64  66  68   2    120.0       505.0    120.0       505.0 ;   CBU  CBV  CBW   
  67  66  68   2    120.0       505.0    120.0       505.0 ;   HBW  CBV  CBW   
  66  68  69   2    120.0       560.0    120.0       560.0 ;   CBV  CBW  NBZ   
  66  68  72   2    120.0       560.0    120.0       560.0 ;   CBV  CBW  CBY   
  69  68  72   2    120.0       560.0    120.0       560.0 ;   NBZ  CBW  CBY   
  68  69  70   2    120.0       390.0    120.0       390.0 ;   CBW  NBZ  HB2   
  68  69  71   2    120.0       390.0    120.0       390.0 ;   CBW  NBZ  HB1   
  70  69  71   2    120.0       445.0    120.0       445.0 ;   HB2  NBZ  HB1   
  68  72  73   2    120.0       505.0    120.0       505.0 ;   CBW  CBY  HBY   
  68  72  74   2    120.0       505.0    120.0       505.0 ;   CBW  CBY  CBX   
  73  72  74   2    120.0       505.0    120.0       505.0 ;   HBY  CBY  CBX   
  63  74  72   2    120.0       505.0    120.0       505.0 ;   CBT  CBX  CBY   
  63  74  75   2    120.0       505.0    120.0       505.0 ;   CBT  CBX  HBX   
  72  74  75   2    120.0       505.0    120.0       505.0 ;   CBY  CBX  HBX   

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
  19  18  20  21   2      0.0  167.4        0.0  167.4   ; imp   CAL  CAN  OAM  CAJ   
  21  19  29  22   2      0.0  167.4        0.0  167.4   ; imp   CAJ  CAL  CAI  CAK   
  22  21  24  23   2      0.0  167.4        0.0  167.4   ; imp   CAK  CAJ  CAE  HAK   
  24  22  25  33   2      0.0  167.4        0.0  167.4   ; imp   CAE  CAK  SAB  CAF   
  25  24  27  26   2     35.3  334.8       35.3  334.8   ; imp   SAB  CAE  OAD  OAC   
  29  21  31  30   2      0.0  167.4        0.0  167.4   ; imp   CAI  CAJ  CAG  HAI   
  31  29  33  32   2      0.0  167.4        0.0  167.4   ; imp   CAG  CAI  CAF  HAG   
  33  34  31  24   2      0.0  167.4        0.0  167.4   ; imp   CAF  NAH  CAG  CAE   
  34  33  35  36   2      0.0  167.4        0.0  167.4   ; imp   NAH  CAF  HAH  CBF   
  36  34  41  37   2      0.0  167.4        0.0  167.4   ; imp   CBF  NAH  CBG  CBJ   
  37  36  39  38   2      0.0  167.4        0.0  167.4   ; imp   CBJ  CBF  CBK  HBQ   
  39  37  45  40   2      0.0  167.4        0.0  167.4   ; imp   CBK  CBJ  CBI  HBR   
  41  36  43  42   2      0.0  167.4        0.0  167.4   ; imp   CBG  CBF  CBH  HBO   
  43  41  45  44   2      0.0  167.4        0.0  167.4   ; imp   CBH  CBG  CBI  HBP   
  45  46  43  39   2      0.0  167.4        0.0  167.4   ; imp   CBI  NBL  CBH  CBK   
  46  45  47  48   2      0.0  167.4        0.0  167.4   ; imp   NBL  CBI  HBZ  CBM   
  48  46  56  49   2      0.0  167.4        0.0  167.4   ; imp   CBM  NBL  CBN  CBO   
  49  48  51  50   2      0.0  167.4        0.0  167.4   ; imp   CBO  CBM  CBP  HBT   
  51  49  52  60   2      0.0  167.4        0.0  167.4   ; imp   CBP  CBO  SCA  CBQ   
  52  51  54  53   2     35.3  334.8       35.3  334.8   ; imp   SCA  CBP  OCD  OCC   
  56  48  58  57   2      0.0  167.4        0.0  167.4   ; imp   CBN  CBM  CBR  HBS   
  58  56  60  59   2      0.0  167.4        0.0  167.4   ; imp   CBR  CBN  CBQ  HBU   
  60  61  58  51   2      0.0  167.4        0.0  167.4   ; imp   CBQ  NBS  CBR  CBP   
  61  60  62  63   2      0.0  167.4        0.0  167.4   ; imp   NBS  CBQ  HB0  CBT   
  63  61  74  64   2      0.0  167.4        0.0  167.4   ; imp   CBT  NBS  CBX  CBU   
  64  63  66  65   2      0.0  167.4        0.0  167.4   ; imp   CBU  CBT  CBV  HBV   
  66  64  68  67   2      0.0  167.4        0.0  167.4   ; imp   CBV  CBU  CBW  HBW   
  68  72  69  66   2      0.0  167.4        0.0  167.4   ; imp   CBW  CBY  NBZ  CBV   
  69  68  71  70   2      0.0  167.4        0.0  167.4   ; imp   NBZ  CBW  HB1  HB2   
  72  68  74  73   2      0.0  167.4        0.0  167.4   ; imp   CBY  CBW  CBX  HBY   
  74  63  72  75   2      0.0  167.4        0.0  167.4   ; imp   CBX  CBT  CBY  HBX   
  63  64  66  68   2      0.0  209.3        0.0  209.3   ; imp   CBT  CBU  CBV  CBW   
  64  66  68  72   2      0.0  209.3        0.0  209.3   ; imp   CBU  CBV  CBW  CBY   
  66  68  72  74   2      0.0  209.3        0.0  209.3   ; imp   CBV  CBW  CBY  CBX   
  68  72  74  63   2      0.0  209.3        0.0  209.3   ; imp   CBW  CBY  CBX  CBT   
  72  74  63  64   2      0.0  209.3        0.0  209.3   ; imp   CBY  CBX  CBT  CBU   
  74  63  64  66   2      0.0  209.3        0.0  209.3   ; imp   CBX  CBT  CBU  CBV   
  48  49  51  60   2      0.0  209.3        0.0  209.3   ; imp   CBM  CBO  CBP  CBQ   
  49  51  60  58   2      0.0  209.3        0.0  209.3   ; imp   CBO  CBP  CBQ  CBR   
  51  60  58  56   2      0.0  209.3        0.0  209.3   ; imp   CBP  CBQ  CBR  CBN   
  60  58  56  48   2      0.0  209.3        0.0  209.3   ; imp   CBQ  CBR  CBN  CBM   
  58  56  48  49   2      0.0  209.3        0.0  209.3   ; imp   CBR  CBN  CBM  CBO   
  56  48  49  51   2      0.0  209.3        0.0  209.3   ; imp   CBN  CBM  CBO  CBP   
  36  37  39  45   2      0.0  209.3        0.0  209.3   ; imp   CBF  CBJ  CBK  CBI   
  37  39  45  43   2      0.0  209.3        0.0  209.3   ; imp   CBJ  CBK  CBI  CBH   
  39  45  43  41   2      0.0  209.3        0.0  209.3   ; imp   CBK  CBI  CBH  CBG   
  45  43  41  36   2      0.0  209.3        0.0  209.3   ; imp   CBI  CBH  CBG  CBF   
  43  41  36  37   2      0.0  209.3        0.0  209.3   ; imp   CBH  CBG  CBF  CBJ   
  41  36  37  39   2      0.0  209.3        0.0  209.3   ; imp   CBG  CBF  CBJ  CBK   
  21  22  24  33   2      0.0  209.3        0.0  209.3   ; imp   CAJ  CAK  CAE  CAF   
  22  24  33  31   2      0.0  209.3        0.0  209.3   ; imp   CAK  CAE  CAF  CAG   
  24  33  31  29   2      0.0  209.3        0.0  209.3   ; imp   CAE  CAF  CAG  CAI   
  33  31  29  21   2      0.0  209.3        0.0  209.3   ; imp   CAF  CAG  CAI  CAJ   
  31  29  21  22   2      0.0  209.3        0.0  209.3   ; imp   CAG  CAI  CAJ  CAK   
  29  21  22  24   2      0.0  209.3        0.0  209.3   ; imp   CAI  CAJ  CAK  CAE   
   4   3   2   1   1      0.0    5.9 3      0.0    5.9 3 ; dih   CBB  CBC  CBD  CBE   
   5   4   3   2   1      0.0    5.9 3      0.0    5.9 3 ; dih   CBA  CBB  CBC  CBD   
   6   5   4   3   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAZ  CBA  CBB  CBC   
   7   6   5   4   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAY  CAZ  CBA  CBB   
   8   7   6   5   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAX  CAY  CAZ  CBA   
   9   8   7   6   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAW  CAX  CAY  CAZ   
  10   9   8   7   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAV  CAW  CAX  CAY   
  11  10   9   8   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAU  CAV  CAW  CAX   
  12  11  10   9   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAT  CAU  CAV  CAW   
  13  12  11  10   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAS  CAT  CAU  CAV   
  14  13  12  11   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAR  CAS  CAT  CAU   
  15  14  13  12   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAQ  CAR  CAS  CAT   
  16  15  14  13   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAP  CAQ  CAR  CAS   
  17  16  15  14   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAO  CAP  CAQ  CAR   
  18  17  16  15   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAN  CAO  CAP  CAQ   
  19  18  17  16   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAL  CAN  CAO  CAP   
  17  18  19  21   1      0.0    1.0 6      0.0    1.0 6 ; dih   CAO  CAN  CAL  CAJ   
  29  21  19  18   1    180.0    5.9 2    180.0    5.9 2 ; dih   CAI  CAJ  CAL  CAN   
  22  24  25  28   1      0.0    4.2 3      0.0    4.2 3 ; dih   CAK  CAE  SAB  OAA   
  24  33  34  36   1    180.0   33.5 2    180.0   33.5 2 ; dih   CAE  CAF  NAH  CBF   
  41  36  34  33   1    180.0   33.5 2    180.0   33.5 2 ; dih   CBG  CBF  NAH  CAF   
  39  45  46  48   1    180.0   33.5 2    180.0   33.5 2 ; dih   CBK  CBI  NBL  CBM   
  56  48  46  45   1    180.0   33.5 2    180.0   33.5 2 ; dih   CBN  CBM  NBL  CBI   
  49  51  52  55   1      0.0    4.2 3      0.0    4.2 3 ; dih   CBO  CBP  SCA  OCB   
  51  60  61  63   1    180.0   33.5 2    180.0   33.5 2 ; dih   CBP  CBQ  NBS  CBT   
  74  63  61  60   1    180.0   33.5 2    180.0   33.5 2 ; dih   CBX  CBT  NBS  CBQ   
  66  68  69  71   1    180.0   33.5 2    180.0   33.5 2 ; dih   CBV  CBW  NBZ  HB1